...
Description | OPTIONAL dotplot of the WGA |
Command | structural_pangenome render-dotplot filtered_delta_file -o output_file OR structural_pangenome render-dotplot filtered_delta_file -p prefix_folder |
| haptic command | haptic render-dotplot filtered_delta_file -o output_file OR haptic render-dotplot filtered_delta_file -p prefix_folder |
Parameters | o: output filename (with complete path) (PREFIX) p: prefix_folder which stores the resulting output file (with complete path) (OUTPUT) |
Input | Assembly fasta filtered delta file (DELTA) - From Step5. |
output | · Assembly Fasta gp file · Assembly Fasta rplot file · Assembly Fasta fplot file · Assembly Fasta PNG file |
| Usage | structural_pangenome render-dotplot [-h] (-p PREFIX | -o OUTPUT) DELTA |
Example | structural_pangenome render-dotplot deltas/assembly_1_vs_pangenome__fasta_bbmhFilter.delta -p outputs/dotplot |
| haptic example | haptic render-dotplot deltas/assembly_1_vs_pangenome__fasta_bbmhFilter.delta -p outputs/dotplot |
Can be Parallelized | Yes |
Optional | Yes |
...
| Description | y |
| Command | structural_pangenome reverse-delta assembly_1_vs_pangenome__fasta_bbmhFilter.delta -o pangenome__fasta_vs_assembly_1_bbmhFilter.delta |
| Parameters | o: output filename (with complete path) (PREFIX) p: prefix_folder which stores the resulting output file (with complete path) (OUTPUT) |
| Input | Assembly fasta filtered delta file (FILE) - From Step6. |
| output | Reverse filtered delta file (OUTPUT) |
| Usage | structural_pangenome reverse-delta [-h] (-p PREFIX | -o OUTPUT) FILE |
| Example | structural_pangenome reverse-delta filtered_deltas/_assembly1_v1_bbmh-filter.delta -o reversed_filtered_deltas/ pangenome__fasta_vs_assembly_1_bbmhFilter.delta |
| Can be parallelized | Yes |
| Optional | No |
...
Description | Create the coordinate pangenome system in JSON |
Command | structural_pangenome build-coordinate reverse_filtered_delta_file -o output_file OR structural_pangenome build-coordinate delta_file -p prefix-folder |
| haptic command | haptic build-json reverse_filtered_delta_file -o output_file OR haptic build-json delta_file -p prefix-folder |
Parameters | o: output filename (with complete path) p: prefix_folder which stores the resulting output file (with complete path) unzipped, optional: set this flag to generated an uncompressed file (–unzipped) pretty, optional: set this flag to generated a json file that is human readable (–pretty) m, optional: metrics, Whether to save coordinate metrics. Filename auto-generated if not given (-m) |
Input | Reversed filtered delta file(s) (DELTA) (DELTA ..), - From Step7. |
output | Pangenome coordinate JSON file (OUTPUT) |
Example | structural_pangenome build-coordinate deltas/pangenome__fasta_vs_assembly_1_bbmhFilter.delta o outputs/coordinate_json.json --pretty --unzipped -m |
| haptic example | haptic build-json deltas/pangenome__fasta_vs_assembly_1_bbmhFilter.delta -o outputs/coordinate-json.json |
| Usage | structural_pangenome build-coordinate [-h] (-p PREFIX | -o OUTPUT) [–unzipped] [--pretty] [-m [METRICS]] DELTA [DELTA ...] |
Can be Parallelized | Yes |
Optional | No |
...
Description | Get the sequence length distribution of the pangenome segment with coordinate in the pangenome |
Command | structural_pangenome find-coordinate-seqlen pangenome_coordinate_file sequence_lengths_file -o output_file -g OR structural_pangenome find-coordinate-seqlen pangenome_coordinate_file sequence_lengths_file -p prefix_folder -g |
| haptic command | haptic find-seqlen reverse_filtered_delta_file -o output_file -g OR haptic find-seqlen reverse_filtered_delta_file -p prefix_folder -g |
Parameters | o: output filename (with complete path) p: prefix_folder which stores the resulting output file (with complete path) g: optional, apply to yield generate sequence length distribution graph |
Input | pangenome coordinate file (COORDINATE) - From Step8. sequence lengths file (.csv) (SEQLEN) - From Step2.4 |
output | pangenome_coordinate_seqLength Graph (OUTPUT) |
| Usage | structural_pangenome find-coordinate-seqlen [-h] (-p PREFIX | -o OUTPUT) [-g] COORDINATE SEQLEN |
Example | structural_pangenome find-coordinate-seqlen Step8.CoordPangenome/coordAssem_pangenome.json Step2.4.seqLens/pangenome__fasta_seqlen.csv -p outputs/seqlenPangenome -g |
| haptic example | haptic find-seqlen deltas/pangenome__fasta_vs_assembly_1_bbmhFiter.delta -p outputs/seqlen |
Can be Parallelized | Yes |
Optional | Yes |
...
| Description | Builds a pangenome path json file, based on the coordinate json file |
| Command | structural_pangenome build-path pangenome_coordinate_json_file -o output file |
| Parameters | o: output filename (with complete path) p: prefix_folder which stores the resulting output file (with complete path) unzipped, optional: set this flag to generated an uncompressed file (–unzipped) pretty, optional: set this flag to generated a json file that is human readable (–pretty) |
| Input | pangenome coordinate JSON file (JSON) - From Step8. |
| output | pangenome path JSON FILE (OUTPUT) |
| Usage | structural_pangenome build-path [-h] (-p PREFIX | -o OUTPUT) [–unzipped] [–pretty] JSON |
| Example | structural_pangenome build-path Step8.CoordPangenome/coordAssem_pangenome.json -o 10.PathPangenome/path__pangenome.json --unzipped --pretty |
| Can be Parallelized | Yes |
| Optional | No |
...